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Yellowhorn (Xanthoceras sorbifolium), especially its varieties, is the red petal yellowhorn (X. sorbifolium var. purpurea), an important tree species with great ornamental value, and its flower petals change color throughout the flowering period. In this study, we mainly focused on the mechanism of the petal color change with transcriptomics and metabolomics data. A phased chromosome-scale assembly of the red petal yellowhorn genome was generated using the PacBio high-fidelity reads, Illumina short reads, and Phase genomics Proximo Hi-C data. The final de novo assembly yielded 533.67 Mb with a contig N50 of 5.42 Mb, and 27 501 protein-coding genes were predicted. Notably, an alternate haplotig assembly was also obtained. Furthermore, a variation database for the alleles within the genome was constructed. Subsequently, the expression pattern of flower pigmentation-related genes and allelic expression imbalance events were investigated. Apart from 6 genes involved in the anthocyanin biosynthesis pathway regulated by the activation of 15 MYB-bHLH-WD40s, the increased expression of senescence-related gene 1 (SRG1) and 2-oxoglutarate-dependent dioxygenase (DIOX5) might also result in decreasing content of lutein and increasing abundance of (E/Z)-phytoene, cyanidin-3-O-rutinoside, and cyanidin-3-O-sambubioside. These changes in genes and metabolites were most likely related to the petal color change in red petal yellowhorn. This phased chromosome-scale genome assembly provides more accurate genomic information for future molecular breeding and facilitates allele function studies of the red petal yellowhorn.

In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which polymorphisms are detected but not assigned to one or the other of the homologous chromosomes. Yet chromosomal phase information is invaluable for the understanding of phenotypic trait inheritance in the cases of compound heterozygosity, allele-specific expression or cis-acting variants. Here we use a combination of tools and sequencing technologies to generate a de novo diploid assembly of the human primary cell line WI-38. First, data from PacBio single molecule sequencing and Bionano Genomics optical mapping were combined to generate an unphased assembly. Next, 10x Genomics linked reads were combined with the hybrid assembly to generate a partially phased assembly. Lastly, we developed and optimized methods to use short-read (Illumina) sequencing of flow cytometry-sorted metaphase chromosomes to provide phase information. The final genome assembly was almost fully (94%) phased with the addition of approximately 2.5-fold coverage of Illumina data from the sequenced metaphase chromosomes. The diploid nature of the final de novo genome assembly improved the resolution of structural variants between the WI-38 genome and the human reference genome. The phased WI-38 sequence data are available for browsing and download at wi38.research.calicolabs.com. Our work shows that assembling a completely phased diploid genome de novo from the DNA of a single individual is now readily achievable.